title: MOE, iRhom2-/-, 5wks, rep2

first: Carl

last: Blobel

address: 515 East 71st street

institute: Hospital for Special Surgery, Research Institute

description: 8KO02wk5 (core ref # 15620)

data_processing:
using nf-core star rsem
Assembly: GRCm38
Supplementary files format and content: csv files of raw counts with differentially expressed logFC and FDR generated by EdgeR

source_name: main olfactory epithelium (MOE)

extract_protocol:
RNA was harvested using the RNEasy Plus Kit (Qiagen) with DnaseI on-column digestion
NEB Ultra II Directional RNA Library Prep (plus Poly A isolation module)

treatment_protocol: Mice were untreated, sacrificed at the stated age, and main olfactory epithelium was dissected.

value: main olfactory epithelium (MOE)

tag: strain

value: mixed

value: M

tag: age

value: 5 weeks old


title: MOE, iRhom2-/-, 30wks, rep1

status: Public on May 28 2024

type: SRA

city: New York

state: New York

country: USA

description: 10KO04wk30 (core ref # 15620)

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: Sex

value: 30 weeks old


title: MOE, WT, 5wks, rep3

description: 3WT03wk5 (core ref # 15620)

value: WT


title: MOE, iRhom2-/-, 30wks, rep2

description: 11KO05wk30 (core ref # 15620)


title: MOE, WT, 30wks, rep3

description: 6WT06wk30 (core ref # 15620)


title: MOE, WT, 30wks, rep2

description: 5WT05wk30 (core ref # 15620)


title: MOE, WT, 30wks, rep1

description: 4WT04wk30 (core ref # 15620)


title: MOE, WT, 8wks, rep3

description: WT6  (core ref # 15045)

value: F

value: 8 weeks old


title: MOE, WT, 5wks, rep1

description: 1WT01wk5 (core ref # 15620)


title: MOE, WT, 5wks, rep2

description: 2WT02wk5 (core ref # 15620)


title: MOE, iRhom2-/-, 30wks, rep3

description: 12KO06wk30 (core ref # 15620)


title: MOE, WT, 8wks, rep2

description: WT5  (core ref # 15045)


title: MOE, WT, 10wks, rep2

description: WT2  (core ref # 14025)

value: 10 weeks old


title: MOE, WT, 8wks, rep1

description: WT4 (core ref # 15045)


title: MOE, WT, 10wks, rep1

description: WT1 (core ref # 14025)


title: day07_6GyIndo_05

city: Frederick

first: David

last: Wink

state: MD

address: 1050 Boyles St

department: CCR

institute: NCI

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (Mouse_mm10) and the annotated transcripts using STAR.
Partek Flow v.11.0.24.0328
FASTQ file
Paired-ended FASTq files were uploaded to the in-house Partek Flow server for subsequent data processing.
RNAseq data were normalized with the Counts per million (CPM)+1 method before differential expression gene detection with ene Specific Analysis (GSA).
Data Matrix were exported to Microsoft Excel 365 (64-bit) for data exploration and heatmap generation
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: 4T1 tumor

growth_protocol: 4T1 murine mammary carcinoma cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum and antibiotics in a humidified atmosphere with 5% CO2 at 37C; 4T1 mice were housed at the accredited facility with a 12-hr day/night cycle.

extract_protocol:
RNAs were harvested using the Qiagen RNeasy Plus Mini kit. 1 ug of total RNA was used for the sequencing library construction.
RNA libraries for total RNA-seq were prepared using Illumina TruSeq Stranded Total RNA Library Prep following the manufacturer's protocol.

treatment_protocol: At the age of 8 weeks, mice were implanted with 200k 4T1 cells at the right hind limb. Mice were randomly divided into different groups when their tumor reached 100–200 mm3. Radiation groups will receive 6 Gy of single-dose irradiation. Indomethacin groups will receive 30 mg/L of indomethacin in drinking water during the whole experimental period.

value: 4T1 tumor

tag: cell line

tag: cell type

value: epithelial

tag: treatment


title: MOE, iRhom2-/-, 5wks, rep1

description: 7KO01wk5 (core ref # 15620)


title: MOE, iRhom2-/-, 10 wks, rep1

description: KO1 (core ref # 14025)


title: day03_6GyIndo_04


title: MOE, WT, 10wks, rep3

description: WT3  (core ref # 14025)


title: day03_6GyIndo_03


title: MOE, iRhom2-/-, 8 wks, rep3

description: KO6  (core ref # 15045)


title: MOE, iRhom2-/-, 5wks, rep3

description: 9KO03wk5 (core ref # 15620)


title: MOE, iRhom2-/-, 8 wks, rep2

description: KO5  (core ref # 15045)


title: MOE, iRhom2-/-, 10 wks, rep2

description: KO2 (core ref # 14025)


title: MOE, iRhom2-/-, 10 wks, rep3

description: KO3 (core ref # 14025)


title: day23_6GyIndo_05


title: MOE, iRhom2-/-, 8 wks, rep1

description: KO4  (core ref # 15045)


title: day23_6GyIndo_01


title: day15_6GyIndo_01


title: day23_6GyIndo_03


title: day03_6GyIndo_02


title: day23_6GyIndo_02


title: day15_6GyIndo_02


title: day15_6GyIndo_05


title: day07_6GyIndo_03


title: day01_6GyIndo_05


title: day07_6GyIndo_01


title: day01_6GyIndo_01


title: day07_6GyIndo_04


title: day07_6GyIndo_02


title: day03_6GyIndo_01


title: day01_6GyIndo_02


title: day01_6GyIndo_03


title: day03_Indo_05


title: day01_Indo_05


title: day23_6GyIndo_04


title: day01_Indo_03


title: day23_Indo_05


title: day15_6GyIndo_03


title: day01_Indo_04


title: day23_Indo_04


title: day23_Indo_02


title: day01_6GyIndo_04


title: day15_Indo_05


title: day15_Indo_03


title: day23_Indo_03


title: day15_Indo_04


title: day07_Indo_02


title: day15_Indo_02


title: day23_Indo_01


title: day07_Indo_03


title: day07_Indo_05


title: day07_Indo_01


title: day07_Indo_04


title: day15_6GyIndo_04


title: day01_Indo_02


title: day03_Indo_03


title: day03_Indo_01


title: day01_Indo_01


title: day03_Indo_04


title: day03_Indo_02


title: day03_6Gy_04


title: day15_Indo_01


title: day07_6Gy_05


title: day15_6Gy_05


title: day01_6Gy_04


title: day03_6Gy_05


title: day23_6Gy_05


title: day07_6Gy_03


title: day07_6Gy_04


title: day23_6Gy_03


title: day23_6Gy_02


title: day15_6Gy_02


title: day15_6Gy_03


title: day23_6Gy_04


title: day23_6Gy_01


title: day01_6Gy_05


title: day07_6Gy_01


title: day03_6Gy_01


title: day03_6Gy_03


title: day01_6Gy_02


title: day01_6Gy_01


title: day03_6Gy_02


title: day07_control_05


title: day07_6Gy_02


title: day15_control_03


title: day23_control_02


title: day03_control_05


title: day15_6Gy_04


title: day23_control_01


title: day15_6Gy_01


title: day01_control_04


title: Mouse blastocysts cultured from E1.5 to 4.5 in M16 medium with 0.00125% Patent Blue, Replicate 2

city: Kagoshima

first: Sumito

last: Matsuya

address: 1-21-24 Korimoto

department: Joint Faculty of Veterinary Medicine

country: Japan

institute: Kagoshima university

data_processing:
The raw data of the sequences were converted to sequence reads using Torrent suite software. The trimmed reads were mapped to the AmpliSeq_Mouse Transcriptome_V1_Reference.fasta using a Torrent mapping aligment program with default setting.
Assembly: AmpliSeq_Mouse_Transcriptome_V1_Reference.fasta
Supplementary files format and content: raw gene count for each amplicon annotated with gene symbol and each sample.

source_name: Blastocysts

growth_protocol: The embryos collected at E1.5 from BDF1 were cultured to blastocysts.

extract_protocol:
Total RNA was isolated using ReliaPrep RNA Cell MiniPrep System (Promega).
Ion Ampliseq Transcriptome Mouse Gene Expression Kit (Life technologies), Ion Ampliseq Transcriptome Mouse Gene Expression Core Panel (Life technologies) and Ion Barcode Adaptors 33-48 Kit (Life technologies) were used for the construction of seqeuncing libraries. Libraries were ampified on beads by emulsion PCR using Ion Chef system (Life technologies). Sequencing was performed with Ion540 Kit Che (Life technologies) and Ion 540 Chip.

treatment_protocol: The collected embryos were cultured in the respective culture media.

value: Blastocysts

value: WT (embryos collected from BDF1 x BDF1)


title: Mouse blastocysts cultured from E1.5 to 4.5 in M16 medium with 0.00125% Patent Blue, Replicate 1


title: day07_control_02


title: day07_control_03


title: day07_control_01


title: day01_6Gy_03


title: KP, replicate 3, scRNA-seq

city: Houston

first: Chaohao

last: Li

state: TX

address: 1881 East Rd

institute: MD Anderson Cancer Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Single-cell RNA-seq gene expression libraries were mapped to mm10 mouse reference (10x Genomics pre-built reference, mm10-2020-A) using Cell Ranger (v6.1.1, 10x Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

growth_protocol: Standard housing condition

extract_protocol:
Single cell suspensions were prepared following 10x Genomics Cell Preparation Guide. Briefly, mice lung tissues were harvested and cut into smaller pieces, then used pipette to extensively pipette up and down to get tissue mixture in DMEM medium containing 2% FBS. This mixture was filtered with a 70 μm nylon mesh strainer, centrifuged at 300 g for 10 mins, then resuspended in DMEM medium containing 2% FBS to get single cell suspension. The single cell suspension was further sorted to enrich immune cell populations, and this suspension was processed for single-cell sequencing. Cell viability was at least 95% for all samples. 10000 cells were targeted for sequencing and loaded onto a Chromium Controller (10x Genomics) for gel beads-in-emulsion formation.
Library preparation was conducted using Chromium Next GEM Single Cell 3’ Gene Expression Kit (v3.1, 10x Genomics) according to the manufacturer’s instructions.

treatment_protocol: Adenovirus-expressing Cre recombinase at a viral titer of 2.5 × 10^7PFU per mouse to induce lung cancer.

value: Lung

value: KP

value: Tumor

value: Ad-Cre


title: Mouse blastocysts cultured from E1.5 to 4.5 in M16 medium with 0.02% Naphtol Green B, Replicate 1


title: day15_control_01


title: day03_control_04


title: Mouse blastocysts cultured from E1.5 to 4.5 in M16 medium with 0.02% Naphtol Green B, Replicate 2


title: Mouse blastocysts cultured from E1.5 to 4.5 in M16 medium with 0.01% Indigo Carmine, Replicate 1


title: day03_control_03


title: day03_control_02


title: Mouse blastocysts cultured from E1.5 to 4.5 in M16 medium with 0.01% Fast Green FCF, Replicate 2


title: day23_control_03


title: day03_control_01


title: Mouse blastocysts cultured from E1.5 to 4.5 in M16 medium with 0.01% Fast Green FCF, Replicate 1


title: day01_control_03


title: Mouse blastocysts cultured from E1.5 to 4.5 in M16 medium with 0.005% Evans Blue, Replicate 1


title: day15_control_02


title: Mouse blastocysts cultured from E1.5 to 4.5 in M16 medium with 0.005% Evans Blue, Replicate 2


title: day07_control_04


title: Mouse blastocysts cultured from E1.5 to 4.5 in M16 medium with 0.01% Brillinat Blue FCF, Replicate 2


title: day01_control_01


title: Mouse blastocysts cultured from E1.5 to 4.5 in M16 medium with 0.01% Brillinat Blue FCF, Replicate 1


title: uvb, contra, replicate 22

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description: uvb, contra, replicate 22

data_processing:
Cell Ranger from 10x Genomics was used for alignment and quantification
Assembly: mm10
Supplementary files format and content: Barcodes, features, and count matrix, in the forms of tab-separated values and market exchange format, in a zipped file for each sample

source_name: Plantar Skin

extract_protocol:
Immune cells are sorted cells from mouse plantar skin at different times.
The scRNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3' Reagent Kit v3.1 following the manufacturer's instructions (10X Genomics).

value: Plantar Skin

value: CD45+ immune cells

tag: condition

value: uvb, contra


title: Mouse blastocysts cultured from E1.5 to 4.5 in mWM medium, Replicate 2

value: cultured from E1.5 to 4.5 in mWM medium


title: Mouse blastocysts cultured from E1.5 to 4.5 in M16 medium with 0.02% Acid Green 3, Replicate 1


title: uvb, contra, replicate 24

description: uvb, contra, replicate 24


title: uvb, contra, replicate 21

description: uvb, contra, replicate 21


title: uvb, contra, replicate 20

description: uvb, contra, replicate 20


title: Mouse blastocysts cultured from E1.5 to 4.5 in mWM medium, Replicate 1


title: Ctrl, replicate 1, RNA_seq

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

country: China

institute: Shandong University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis.
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-4.7). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: colon

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon

value: immune cell

value: Control


title: Mouse blastocysts cultured from E1.5 to 4.5 in KSOM medium, Replicate 2


title: Mouse blastocysts cultured from E1.5 to 4.5 in KSOM medium, Replicate 1


title: uvb, contra, replicate 18

description: uvb, contra, replicate 18


title: uvb, contra, replicate 19

description: uvb, contra, replicate 19


title: uvb, contra, replicate 23

description: uvb, contra, replicate 23


title: Mouse blastocysts cultured from E1.5 to 4.5 in M16 medium, Replicate 2

value: cultured from E1.5 to 4.5 in M16 medium


title: uvb, contra, replicate 17

description: uvb, contra, replicate 17


title: Mouse blastocysts cultured from E1.5 to 4.5 in M16 medium, Replicate 1


title: incision, 48h, replicate 2

description: incision, 48h, replicate 2

value: incision, 48h


title: LUAD, tumor, pair 65

type: genomic

city: Guangzhou

first: Man

last: Shu

state: Guangdong

address: No.58 Zhongshan Er Road

institute: the First Affiliated Hospital of Sun Yat-sen University

description:
LUAD tumor sample
205103220004_R03C01

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium  MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
genomestudio software 1.0
Matrix process.txt = normalized (Beta MIxture Quantile dilation, BMIQ) Average Beta
Matrix signal intensities.txt = Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: fresh tissue

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LUAD samples using QIAamp DNA mini kit according to standard instructions

tag: paired tissue

tag: sample type

value: LUAD

tag: disease state

value: tumor

value: female

tag: t grade

tag: Stage

value: II


title: LUAD, tumor, pair 64

description:
LUAD tumor sample
205062750003_R06C01

value: I


title: incision, 24h, replicate 2

description: incision, 24h, replicate 2

value: incision, 24h


title: LUAD, tumor, pair 63

description:
LUAD tumor sample
205055450063_R06C01


title: LUAD, tumor, pair 61

description:
LUAD tumor sample
205062750003_R04C01


title: incision, 4h, replicate 2

description: incision, 4h, replicate 2

value: incision, 4h


title: incision, 48h, replicate 1

description: incision, 48h, replicate 1


title: LUAD, tumor, pair 62

description:
LUAD tumor sample
205103220004_R04C01

value: III


title: incision, contra, replicate 2

description: incision, contra, replicate 2

value: Plantar Skin

value: incision, contra


title: incision, 24h, replicate 1

description: incision, 24h, replicate 1

value: CD45+ immune cells


title: incision, 4h, replicate 1

description: incision, 4h, replicate 1


title: LUAD, tumor, pair 57

description:
LUAD tumor sample
205062750003_R03C01


title: day01_control_02

value: 4T1 tumor

value: epithelial


title: LUAD, tumor, pair 58

description:
LUAD tumor sample
205111140008_R08C01

value: male


title: incision, contra, replicate 1

description: incision, contra, replicate 1


title: LUAD, tumor, pair 59

description:
LUAD tumor sample
205055450063_R01C01


title: LUAD, tumor, pair 56

description:
LUAD tumor sample
205111140008_R02C01


title: LUAD, tumor, pair 55

description:
LUAD tumor sample
205097260085_R08C01


title: LUAD, tumor, pair 54

description:
LUAD tumor sample
205097260085_R06C01

value: IV


title: zymosan, 4h, replicate 2

description: zymosan, 4h, replicate 2

value: zymosan, 4h


title: zymosan, contra, replicate 2

description: zymosan, contra, replicate 2

value: zymosan, contra


title: LUAD, tumor, pair 53

description:
LUAD tumor sample
205062750003_R05C01

value: LUAD


title: zymosan, 48h, replicate 1

description: zymosan, 48h, replicate 1

value: zymosan, 48h


title: LUAD, tumor, pair 52

description:
LUAD tumor sample
205062750003_R01C01

value: tumor

value: female


title: zymosan, 4h, replicate 1

description: zymosan, 4h, replicate 1


title: zymosan, contra, replicate 1

description: zymosan, contra, replicate 1


title: LUAD, tumor, pair 50

description:
LUAD tumor sample
205097260085_R01C01


title: PD-1_CTLA-4_d21_5

city: Osaka

first: Koji

last: Nagaoka

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Immunology

institute: Kindai University Faculty of Medicine

data_processing:
Sequence reads were mapped to mm10 using STAR(version 2.7.0f).
Mapped reads were counted by FeatureCounts (version 1.6.4 ).
Genome_build: mm10
Supplementary_files_format_and_content: raw count
Assembly: mm10
Supplementary files format and content: csv file including raw counts

source_name: Tumor tissue

extract_protocol:
Total RNA was isolated from tumor tissues using TRIzol (Thermo Fisher Scientific, Waltham, Massachusetts, USA) and RNeasy spin columns (Qiagen, Venlo, The Netherlands) according to the manufacturer's protocols.
Libraries were prepared using Illumina NEBNext Ultra II RNA Library Prep Kit for Illumina according to the manufacturer's protocols.

value: Tumor tissue

value: anti-PD-1 and anti-CTLA-4


title: LUAD, tumor, pair 60

description:
LUAD tumor sample
205055450063_R03C01

value: I


title: LUAD, tumor, pair 48

description:
LUAD tumor sample
205111140014_R06C01


title: PD-1_CTLA-4_d21_4


title: PD-1_CTLA-4_d21_3


title: LUAD, tumor, pair 51

description:
LUAD tumor sample
205062750048_R08C01


title: LUAD, tumor, pair 49

description:
LUAD tumor sample
205111140014_R08C01


title: LUAD, tumor, pair 47

description:
LUAD tumor sample
205111140014_R04C01


title: zymosan, 24h, replicate 2

description: zymosan, 24h, replicate 2

value: zymosan, 24h


title: LUAD, tumor, pair 46

description:
LUAD tumor sample
205111140014_R02C01


title: LUAD, tumor, pair 45

description:
LUAD tumor sample
205062750048_R07C01


title: PD-1_CTLA-4_d21_2


title: zymosan, 48h, replicate 2

description: zymosan, 48h, replicate 2

value: Plantar Skin


title: Control_d21_5

value: Untreated


title: PD-1_CTLA-4_d21_1


title: LUAD, tumor, pair 42

description:
LUAD tumor sample
205049770052_R03C01


title: LUAD, tumor, pair 44

description:
LUAD tumor sample
205049770052_R07C01


title: Control_d21_4


title: Control_d21_2


title: LUAD, tumor, pair 43

description:
LUAD tumor sample
205049770052_R05C01

value: II


title: LUAD, tumor, pair 41

description:
LUAD tumor sample
205111140051_R08C01


title: zymosan, 24h, replicate 1

description: zymosan, 24h, replicate 1

value: CD45+ immune cells


title: Control_d21_3


title: Control_d21_1


title: LUAD, tumor, pair 40

description:
LUAD tumor sample
205111140051_R07C01


title: LUAD, tumor, pair 39

description:
LUAD tumor sample
205111140051_R06C01


title: Control_d35_4


title: LUAD, tumor, pair 38

description:
LUAD tumor sample
205062750003_R08C01


title: LUAD, tumor, pair 37

description:
LUAD tumor sample
205113580126_R03C01


title: Control_d35_5


title: LUAD, tumor, pair 36

description:
LUAD tumor sample
205062750057_R03C01


title: Control_d35_2


title: Control_d35_3


title: LUAD, tumor, pair 35

description:
LUAD tumor sample
205062750048_R06C01


title: LUAD, tumor, pair 34

description:
LUAD tumor sample
205062750057_R01C01


title: LUAD, tumor, pair 32

description:
LUAD tumor sample
205062750003_R07C01


title: PD-1_CTLA-4_d35_4


title: LUAD, tumor, pair 33

description:
LUAD tumor sample
205103220094_R07C01


title: LUAD, tumor, pair 31

description:
LUAD tumor sample
205103220094_R05C01


title: PD-1_CTLA-4_d35_2


title: PD-1_CTLA-4_d35_1


title: CTLA-4_d35_3


title: LUAD, tumor, pair 29

description:
LUAD tumor sample
205103220094_R03C01


title: CTLA-4_d35_4


title: CTLA-4_d35_1


title: CTLA-4_d35_2


title: Control_d35_1


title: LUAD, tumor, pair 24

description:
LUAD tumor sample
205113580134_R03C01


title: LUAD, tumor, pair 23

description:
LUAD tumor sample
205062750039_R07C01


title: LUAD, tumor, pair 22

description:
LUAD tumor sample
205062750048_R05C01


title: PD-1_d35_2


title: PD-1_d35_3


title: PD-1_CTLA-4_d35_5


title: LUAD, tumor, pair 26

description:
LUAD tumor sample
205113580134_R05C01


title: 2445187_aFoxp3_Tumor_2

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

library_source: genomic

data_processing:
library strategy: Cut&Tag
Trim_Galore(v0.4.4) is used to quality trim 3’ reads raw reads with the cutadapt (DOI: 10.14806/ej.17.1.200) program. A quality score cutoff of Q20 is used. 15bp from 5' were also trimmed to reduce Tn5 bias.
Trimmed reads are mapped to the mm10(Gencode GRCm38) reference genome by bwa(v0.7.12-r1039, PMID: 19451168) and converted to a bam file(a binary version of sam file) by samtools(v1.2, PMID: 19505943).
biobambam2 (v2.0.87, DOI: 10.1186/1751-0473-9-13) was used to mark duplicated reads and non-duplicated reads were kept by samtools (parameter “-q 1 -F 1804” version 1.2).
All samples have more than 4 million fragments as CUT&TAG protocol paper suggested > 3 million. We generated bigwig files using the center 80 bp of fragments smaller than 2000 bp and normalized to 10 million fragments. We confirmed the replicability between replicates.
Assembly: mm10(Gencode GRCm38)
Supplementary files format and content: bigwig

source_name: Tumor

extract_protocol:
CD4 T cells were enriched by EasySep Mouse CD4 T Cell Isolation Kit (STEMCELL) from lymph nodes and spleens. CD4 naïve T cells (Tn: CD4+ CD25-CD44loCD62Lhi), natural Treg cells (CD4+GFP+) T cells, CD4 effector T cells (Te, CD4+GFP-CD44hiCD62Llo), resting Treg cells (rTreg: CD4+GFP+CD44loCD62Lhi), activated Treg cells (aTreg: CD4+ GFP+CD44hiCD62Llo) were further sorted by FACS.
Libraries were prepared with precipitated DNA using KAPA Hyper Prep Kit (Kapa Biosystems). The library DNA was enriched by size selection with AMPure XP beads.

value: Tumor

value: tumor infiltrating Treg

value: No


title: LUAD, tumor, pair 28

description:
LUAD tumor sample
205062750027_R02C01


title: LUAD, tumor, pair 25

description:
LUAD tumor sample
205113580134_R02C01

value: male


title: 2317026_aFoxp3-TregTCR_3h-1

source_name: Spleen and lymph nodes

value: Spleen and lymph nodes

value: resting Treg


title: PD-1_d35_5


title: PD-1_d35_4


title: PD-1_d35_1


title: PD-1_CTLA-4_d35_3


title: LUAD, tumor, pair 20

description:
LUAD tumor sample
205062750057_R04C01

value: LUAD

value: III


title: LUAD, tumor, pair 13

description:
LUAD tumor sample
205113580134_R01C01

value: tumor


title: 2317019_aFoxp3-Treg0h-2

value: Mock (DPBS)


title: 2317017_aFoxp3-aTreg-2

value: activated Treg


title: LUAD, tumor, pair 30

description:
LUAD tumor sample
205113580126_R01C01

value: I


title: 2317018_aFoxp3-Treg0h-1


title: LUAD, tumor, pair 12

description:
LUAD tumor sample
205062750048_R04C01

value: female


title: LUAD, tumor, pair 27

description:
LUAD tumor sample
205113580134_R06C01


title: 2445186_aFoxp3_Tumor_1


title: 2317029_aFoxp3-TregIL2_3h-2


title: LUAD, tumor, pair 17

description:
LUAD tumor sample
205103220094_R04C01


title: 2317015_aFoxp3-rTreg-2


title: LUAD, tumor, pair 18

description:
LUAD tumor sample
205103220094_R08C01


title: LUAD, tumor, pair 21

description:
LUAD tumor sample
205062750027_R01C01

value: IV


title: LUAD, tumor, pair 16

description:
LUAD tumor sample
205062750027_R08C01


title: LUAD, tumor, pair 19

description:
LUAD tumor sample
205113580126_R02C01


title: 2317028_aFoxp3-TregIL2_3h-1


title: LUAD, tumor, pair 10

description:
LUAD tumor sample
205113580126_R06C01


title: 2317027_aFoxp3-TregTCR_3h-2


title: 2180956_aGFP-rTreg-2


title: 2317014_aFoxp3-rTreg-1


title: LUAD, tumor, pair 15

description:
LUAD tumor sample
205103220094_R02C01


title: LUAD, tumor, pair 7

description:
LUAD tumor sample
205111140038_R02C01


title: LUAD, tumor, pair 14

description:
LUAD tumor sample
205111140051_R03C01


title: LUAD, tumor, pair 6

description:
LUAD tumor sample
205103220094_R06C01


title: 2180953_aGFP-rTreg-1


title: LUAD, tumor, pair 5

description:
LUAD tumor sample
205111140051_R02C01


title: 2317016_aFoxp3-aTreg-1


title: LUAD, tumor, pair 11

description:
LUAD tumor sample
205062750027_R06C01


title: 2580188_aBatf_sgBatf_TCR_1

data_processing:
Trim_Galore(v0.4.4) is used to quality trim 3’ reads raw reads with the cutadapt (DOI: 10.14806/ej.17.1.200) program. A quality score cutoff of Q20 is used.
Trimmed reads are mapped to the mm10(Gencode GRCm38) reference genome by bwa(v0.7.12-r1039, PMID: 19451168) and converted to a bam file(a binary version of sam file) by samtools(v1.2, PMID: 19505943).
biobambam2 (v2.0.87, DOI: 10.1186/1751-0473-9-13) was used to mark duplicated reads and non-duplicated reads were kept by samtools (parameter “-q 1 -F 1804” version 1.2).
All samples have more than 5 million fragments as suggested by CUT&RUN protocol paper. We generated bigwig files using the center 80 bp of fragments smaller than 2000 bp and normalized to 10 million fragments. We confirmed the replicability between replicates.
Assembly: mm10(Gencode GRCm38)
Supplementary files format and content: bigwig
Library strategy: Cut&Run

extract_protocol:
CD4 T cells were enriched by EasySep Mouse CD4 T Cell Isolation Kit (STEMCELL) from lymph nodes and spleens. Natural Treg cells (CD4+GFP+) T cells, resting Treg cells (rTreg: CD4+GFP+CD44loCD62Lhi), activated Treg cells (aTreg: CD4+ GFP+CD44hiCD62Llo) were further sorted by FACS.
Libraries were prepared with precipitated DNA using KAPA Hyper Prep Kit (Kapa Biosystems). The library DNA was enriched by size selection with AMPure XP beads.

value: ex vivo cultured nTreg cells

value: sgBatf in RosaCas9/+ Foxp3gfp

value: anti-CD3/anti-CD28 restimulation


title: 2580185_aBatf_NC_TCR_2

value: sgNC in RosaCas9/+ Foxp3gfp


title: LUAD, tumor, pair 8

description:
LUAD tumor sample
205111140038_R07C01


title: LUAD, tumor, pair 2

description:
LUAD tumor sample
205103220100_R07C01


title: 2180955_aGFP-aTreg-2


title: 2180952_aGFP-aTreg-1


title: 2580189_aBatf_sgBatf_TCR_2


title: 2570662_aFoxp3_CR_TCR_sgBatf1


title: LUAD, normal, pair 65

description:
normal lung sample
205103220004_R01C01

value: normal

value: II


title: LUAD, normal, pair 63

description:
normal lung sample
205055450063_R05C01


title: 2570659_aFoxp3_CR_TCR_NC2


title: 2570658_aFoxp3_CR_TCR_NC1


title: LUAD, normal, pair 64

description:
normal lung sample
205055450063_R07C01


title: LUAD, normal, pair 62

description:
normal lung sample
205103220004_R02C01


title: LUAD, tumor, pair 9

description:
LUAD tumor sample
205062750057_R08C01

value: male


title: LUAD, tumor, pair 1

description:
LUAD tumor sample
205103220100_R06C01


title: LUAD, tumor, pair 4

description:
LUAD tumor sample
205062750057_R06C01


title: 2580184_aBatf_NC_TCR_1

value: Spleen and lymph nodes


title: LUAD, tumor, pair 3

description:
LUAD tumor sample
205103220100_R08C01


title: 2570663_aFoxp3_CR_TCR_sgBatf2


title: Cold_3h_Rep3

city: Frederiksberg

first: Swetha

last: Chenna

state: Choose State

address: Bülowsvej

country: Denmark

institute: University of Copenhagen

data_processing:
The reads were aligned using STAR v2.7.10a with parameters --outSAMmultNmax 1 --alignEndsType Extend5pOfRead1 --clip3pAdapterSeq AGATCGGAAGAGC.
The reads that aligned below mapping quality of 10 were filtered out using samtools v1.6.
The strand specific coverage was calculated using bedtools (v2.30) genomecov
Assembly: EnsemblePlants v6.54
Supplementary files format and content: Normalised read counts in bedgraph format

organism: Manihot esculenta

source_name: Shoot

growth_protocol: Seedlings were grown in climate chambers with a long day photoperiod (16h light/8h dark cycle) at 20°C/18°C. Light intensity and humidity during control growth conditions was ~100 μE m−2 s−1 and 60% respectively.

extract_protocol:
Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) and treated with Turbo DNase (ThermoFisher Scientific) according to manufacturers’ instructions. DNase-treated RNA was recovered by acid–phenol extraction and ethanol precipitation.
The libraries were prepared from total RNA samples using Lexogen QuantSeq 3' mRNA-seq REV kit following manufacturer's protocol.

treatment_protocol: For cold treatment, seedlings were grown in control conditions for two weeks and subsequently transferred to a cold room (4°C) with light for 3 h before harvesting.

tag: cultivar

value: WT

value: Shoot

value: cold (4 C)

tag: time

value: 3 hours


title: Cold_3h_Rep2


title: Cold_3h_Rep1


title: Cold_3h_Rep4


title: 2523658_CR_Batf_aTreg_2

value: No


title: LUAD, normal, pair 60

description:
normal lung sample
205055450063_R02C01

value: LUAD


title: LUAD, normal, pair 61

description:
normal lung sample
205055450063_R04C01

value: I


title: LUAD, normal, pair 59

description:
normal lung sample
205113580126_R05C01

value: female


title: 2523656_CR_Batf_rTreg_2

value: resting Treg


title: 2523657_CR_Batf_aTreg_1

value: activated Treg


title: WT_Rep1


title: WT_Rep2


title: WT_Rep4


title: LUAD, normal, pair 58

description:
normal lung sample
205062750048_R03C01


title: WT_Rep3


title: LUAD, normal, pair 56

description:
normal lung sample
205111140008_R01C01


title: K562, delEX2, rep3

city: Mexico city

first: Hober

last: Nuñez

state: CDMX

address: Cto. Exterior s/n

department: Molecular Genetics

country: Mexico

institute: IFC-UNAM

data_processing:
Sequencing reads were trimmed for adaptor sequence using Trim Galore
Trimmed sequencing reads were mapped to GRCh37/hg19 using STAR
Read count and normalization were performed using FeatureCounts and EdgeR, respectively.
Assembly: hg19
Supplementary files format and content: Normalized raw signal in bigwig format

source_name: Hematopoietic

growth_protocol: K562 cells were grown in ISCOVE supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) reagent according to the manufacturer's protocol.
mRNA was enriched from total RNA using oligo(dT) beads. First, the mRNA was randomly fragmented by adding fragmentation buffer. Then, cDNA was synthesized using the mRNA as a template and random hexamers primer. A custom second-strand synthesis buffer (Illumina), dNTPs, RNase H, and DNA polymerase I were added to initiate the second-strand synthesis. After a series of terminal repairs, A-tailing, and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

value: Hematopoietic

value: chronic myelogenous leukemia


title: 2523655_CR_Batf_rTreg_1


title: H3_Normoxia

city: guangzhou

first: shengqi

last: shen

address: zhongshan road #104

institute: GDPH

data_processing:
The original sequences were basecalled using the official Oxford Nanopore software Guppy, followed by filtering based on sequence length and quality (length_100, quality_7) to obtain clean data.
Identification of full-length transcripts was performed using Pinfish software. Subsequently, alignment was conducted using Minimap 2 software, followed by clustering based on the alignment results to obtain Consensus sequences
Gffcompare software was used to annotate the Consensus sequences and organize the results, obtaining information on known transcripts and novel transcripts.
The structural analysis includes new gene prediction and database annotation, alternative splicing analysis, novel transcript identification, transcription factor analysis, and LncRNA analysis.
Database functional annotation is performed on the identified novel transcripts.
Differential enrichment analysis includes gene/transcript expression level analysis, differential gene/transcript analysis, as well as GO, KEGG enrichment analysis, and clustering analysis of differential genes.
Assembly: hg38
Supplementary files format and content: tab-delimited txt files include raw counts for each sample

molecule: polyA RNA

source_name: cell line

growth_protocol: Hep3B, and THLE-3 cell lines were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. Cells were kept at 37℃ in humidified 5% CO2 in air. Hypoxia condition was achieved by placing cells in a hypoxic working station which contains 1% O2, 5% CO2, and 94% N2.

extract_protocol:
According to the manufacturer’s instructions, total RNA was extracted from cells or tissues using TRIzol (Life Technologies)
Using the standard adapter-ligation method for library construction, optional DNA fragmentation, end-repair, A-tailing, followed by ligation of sequencing adapters, motor protein, and Tether protein to prepare the cDNA library

treatment_protocol: THLE-3 and Hep3B cell lines were treated for 48h under normoxia or hypoxia and extracted  total mRNA for furthur nanopore sequencing.

value: cell line

value: liver cancer cell

value: Normoxia


title: H3_Hypoxia

value: Hypoxia


title: K562, delEX1, rep3


title: K562, delEX2, rep1


title: 2512257_RNAseq_TCR3h_sgFoxp3_2

description:
RNA.STRANDED_RSEM_gene_TPM.tsv
RNA.STRANDED_RSEM_gene_count.tsv

data_processing:
Paired-end 100-cycle sequencing was performed on NovaSeq6000 sequencer following the manufacturer’s instructions (Illumina).
Raw reads were first trimmed using TrimGalore (v0.6.3) with parameters ‘--paired --retain_unpaired’.
Filtered reads were then mapped to the mm10(Gencode GRCm38) using STAR (v2.7.9a). Gene-level read quantification was done using RSEM (v1.3.1) on the Gencode annotation v31.
Assembly: mm10(Gencode GRCm38)
Supplementary files format and content: raw counts by genes from RSEM
Supplementary files format and content: TPM by genes from RSEM

extract_protocol:
CD4 T cells were enriched by EasySep Mouse CD4 T Cell Isolation Kit (STEMCELL) from lymph nodes and spleens. nTreg cells (CD4+GFP+) were further sorted by FACS
Libraries were prepared by St. Jude Hartwell Genome Sequencing Center using stranded protocol

value: Spleen and lymph nodes

value: ex vivo cultured nTreg cells

value: sgFoxp3 in RosaCas9/+ Foxp3gfp

value: anti-CD3/anti-CD28 restimulation


title: T3_Hypoxia

value: normal liver cell


title: 2512254_RNAseq_TCR0h_sgFoxp3_1

value: Mock (DPBS)


title: 2512256_RNAseq_TCR3h_sgFoxp3_1


title: T3_Normoxia


title: LUAD, normal, pair 54

description:
normal lung sample
205097260085_R05C01

value: LUAD

value: normal

value: IV


title: 2512253_RNAseq_TCR3h_NC_2

value: sgNC in RosaCas9/+ Foxp3gfp


title: 2512255_RNAseq_TCR0h_sgFoxp3_2


title: K562, WT, rep2

value: WT


title: K562, WT, rep1

value: Hematopoietic


title: K562, delEX1, rep2

value: chronic myelogenous leukemia


title: K562, delEX1, rep1


title: LUAD, normal, pair 57

description:
normal lung sample
205111140008_R04C01

value: female

value: I


title: K562, WT, rep3


title: K562, delEX2, rep2


title: K562, WT, ODD, rep2

data_processing:
Sequencing reads were trimmed for adaptor sequence using Trim Galore
Trimmed sequencing reads were mapped to GRCh37/hg19 using Bowtie2
Read filtering and peak calling were performed using NGSUtils and MACS2, respectively.
Assembly: hg19
Supplementary files format and content: Normalized raw signal in bigwig format
Library strategy: ChIRP-seq

extract_protocol:
Cells were crosslinked with 1% Glutaraldehyde for 10 minutes. Chromatin was sheared by sonication. Immunoprecipitation was performed overnight with the corresponding probes. DNA was purified from A/G beads using phenol-chloroform.
ChIRP-seq libraries were prepared using NEBNext Ultra Library Prep Kit for Illumina according to the manufacturer's conditions.

tag: chip antibody

value: Odd probes


title: LUAD, normal, pair 53

description:
normal lung sample
205097260085_R04C01

value: male


title: 2512252_RNAseq_TCR3h_NC_1

value: Spleen and lymph nodes


title: K562, WT, ODD, rep1


title: 2512250_RNAseq_TCR0h_NC_1

value: ex vivo cultured nTreg cells


title: LUAD, normal, pair 50

description:
normal lung sample
205113580126_R07C01

value: III


title: LUAD, normal, pair 52

description:
normal lung sample
205097260085_R03C01


title: K562, WT, Input, rep2

value: Input


title: LUAD, normal, pair 55

description:
normal lung sample
205097260085_R07C01

value: II


title: RTreg_WT_Rep3

data_processing:
100 bp paired-end reads obtained were trimmed by Trim_Galore(v0.4.4) with the cutadapt (DOI: 10.14806/ej.17.1.200) program. Nextera adapters were trimmed and a quality score cutoff of Q20 is used. 15bp from 5' were also trimmed to reduce Tn5 bias.
Trimmed reads are mapped to the mm10(Gencode GRCm38) reference genome by bwa(v0.7.12-r1039, PMID: 19451168) and converted to a bam file(a binary version of sam file) by samtools(v1.2, PMID: 19505943).
biobambam2 (v2.0.87, DOI: 10.1186/1751-0473-9-13) was used to mark duplicated reads and non-duplicated reads were kept by samtools (parameter “-q 1 -F 1804” version 1.2).
We adjust Tn5 shift (reads were offset by +4 bp for the sense strand and -5 bp for the antisense strand) and separated reads into nucleosome free, mononucleosome, dinucleosome, and trinucleosome by fragment size.
We generated bigwig files by using the center 80bp of fragments and scale to 20 million nucleosome free reads. We observed good pattern that nucleosome tracks surrounded nucleosome free tracks, we provided nucleosome free tracks here since they are more informative. All samples have more than 20 million reads as good quality.
Assembly: mm10(Gencode GRCm38)
Supplementary files format and content: bigwig

value: resting Treg

value: No


title: K562, WT, EVEN, rep1

value: Even probes


title: K562, WT, EVEN, rep2


title: LUAD, normal, pair 49

description:
normal lung sample
205111140014_R07C01

value: LUAD

value: normal


title: LUAD, normal, pair 48

description:
normal lung sample
205111140014_R05C01


title: K562, delEX1, H3K27me3, rep2

data_processing:
Sequencing reads were trimmed for adaptor sequence using Trim Galore
Trimmed sequencing reads were mapped to GRCh37/hg19 using Bowtie2
Read filtering and peak calling were performed using NGSUtils and MACS2, respectively.
Assembly: hg19
Supplementary files format and content: Normalized raw signal in bigwig format

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes. Chromatin was sheared by sonication. Immunoprecipitation was performed overnight with the corresponding primary antibody. DNA was purified from A/G beads using phenol-chloroform.
ChIP-seq libraries were prepared using NEBNext Ultra Library Prep Kit for Illumina according to the manufacturer's conditions.


title: K562, delEX1, H3K27ac, rep2


title: RTreg_WT_Rep1


title: LUAD, normal, pair 47

description:
normal lung sample
205111140008_R06C01


title: 2512251_RNAseq_TCR0h_NC_2

value: sgNC in RosaCas9/+ Foxp3gfp

value: Mock (DPBS)


title: K562, delEX1, H3K4me1, rep2

value: Hematopoietic

value: chronic myelogenous leukemia


title: K562, delEX1, H3K27ac, rep1


title: ATreg_WT_Rep2

value: activated Treg


title: ATreg_WT_Rep3


title: LUAD, normal, pair 51

description:
normal lung sample
205097260085_R02C01

value: female

value: I


title: K562, delEX1, H3K4me1, rep1


title: LUAD, normal, pair 46

description:
normal lung sample
205111140014_R01C01

value: male


title: LUAD, normal, pair 45

description:
normal lung sample
205049770052_R08C01


title: K562, WT, Input, rep1


title: ATreg_WT_Rep1

value: Spleen and lymph nodes


title: K562, WT, H3K27me3, rep1


title: LUAD, normal, pair 44

description:
normal lung sample
205049770052_R06C01


title: LUAD, normal, pair 43

description:
normal lung sample
205049770052_R04C01


title: K562, WT, H3K27ac, rep2


title: RTreg_WT_Rep2


title: 2571421_ATACseq_TCR_sgBatf2

value: ex vivo cultured nTreg cells

value: sgBatf in RosaCas9/+ Foxp3gfp

value: anti-CD3/anti-CD28 restimulation


title: K562, delEX1, H3K27me3, rep1


title: K562, WT, H3K27ac, rep1


title: K562, WT, H3K4me1, rep2


title: LUAD, normal, pair 42

description:
normal lung sample
205049770052_R02C01


title: K562, WT, H3K4me1, rep1


title: 2571417_ATACseq_TCR_NC2


title: LUAD, normal, pair 41

description:
normal lung sample
205062750048_R01C01


title: K562, WT, H3K4me3, rep2


title: K562, delEX1, H3K4me3, rep2


title: K562, WT, H3K4me3, rep1


title: K562, delEX1, H3K4me3, rep1


title: H1299_TAF2_ChIP-seq

city: Taipei

first: Wei-Yi

last: Chen

address: No. 155, Sec 2, Linong St.

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the HG19 human genome assembly using bowtie version 1.12 with with parameters "-n 2 -m 1 -l 36 --best". RNA-seq reads were alined to the HG19 human genome sequence using RNA STAR (Galaxy website) with the default parameters.
Potential PCR duplicates in ChIP-seq reads were removed using samtools rmdup command.
Bigwig files were generated by bamCoverage with default parameters in Galaxy plateform.
The gene expression profiling was analyzed by featureCounts and DEseq2 oftwares in Galaxy plateform.
Assembly: HG19
Supplementary files format and content: Bigwig  files for ChIP-seq and RNA-seq samples.

source_name: Non-small cell lung cancer

growth_protocol: The HCT116 lines were maintained in McCoy'5A medium. H1299 and A2780 were maintained in DMEM medium. All cultured medium were supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin and cells were grown at 37°C and 5% CO2

extract_protocol:
Chromatin lysates were prepared by sonication and protein-DNA complexes were isolated with anti-TAF2, anti-TBP (ab28175), anti-H3K4Me3 (ab8580), anti-H3K27Ac (ab4729), anti-H3K4Me (ab8895), and anti-H3K18Ac (ab40888) followed by purification with PCR purification kit (Qiagen). The isolated genomic DNA were subjected to high throughput sequencing service provided by the genomic core facility of Nation Yang Ming Chiao Tung University, Taiwan. Total RNAs were extrated using Quick-RNA  Miniprep kit (Zymo Research) and subjected to RNA-seq service provided by Genomic Core of Institute of Molecular Biology, Academia Sinica, Taiwan.
Multiplexing libraries were prepared for sequencing using Illumina TruSeq Rapid SR Cluster Kit according to the standard protocol.

treatment_protocol: For TAF2 ChIP, wild-type HCT116, A2780, and H1299 were fixed in 1% formaldehyde medium at room temperature followed by 0.125M glycine quenching. For TBP ChIP, TAF2-AID HCT116 cells were incubated in doxycyclin-containing medium was treated without or with IAA for 6 hr or 24 hr and followed by fixation with 1% formaldehyde and quenching with 0.125M glycine. For RNA-seq, HCT116 cells were treated with shScramble or shTAF2 for 144 hours.

value: Non-small cell lung cancer

value: WT

value: TAF2 (custom-made)


title: 2571416_ATACseq_TCR_NC1


title: H1299_input


title: K562, WT, H3K27me3, rep2


title: LUAD, normal, pair 40

description:
normal lung sample
205049770058_R08C01

value: LUAD


title: A2780_TAF2_ChIP-seq

source_name: Ovarian  carcinoma

value: Ovarian  carcinoma


title: ZRS/hs1516 Hindlimb ZPA, E11.5, replicate 4, ATAC-seq

city: Irvine

first: Evgeny

last: Kvon

address: 4310 McGaugh Hall

department: Developmental and Cell Biology

institute: University of California, Irvine

description: Processed data are available on Rep 1 sample.

data_processing:
Fastq files were trimmed and clipped using trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using the following options -q 20 --stringency 2 --clip_R1 16 --clip_R2 16. Reads were then aligned to the original mm10 genome assembly as well as to a modified version of the genome containing the corresponding insertion using bedtools getfasta (Quinlan & Hall, 2010).
Assembly: mm10 + custom chr5 (hs1516/ZRS)

source_name: FVB (strain)

extract_protocol:
Posterior limb bud tissue containing the ZPA region from E11.5 mouse embryos was dissected and manually disassociated followed by snap freezing.
Library construction was performed using the Omni-ATAC-seq protocol (Buenrostro et al., 2013, 2015), with an adjusted lysis step and transposition buffer based on Omni-ATAC protocol (Corces et al., 2017).

value: FVB (strain)

value: Hindlimb

tag: read size


title: ZRS/hs1516 Hindlimb ZPA, E11.5, replicate 2, ATAC-seq


title: HCT116_IAA_6hr_TBP_ChIP-seq

source_name: Colorectal carcinoma

value: Colorectal carcinoma

value: mAID knockin at TAF2 locus, rtTA3 expressing, Doxycline-inducible expression of OsTIR1

value: Doxycyclin and 6 hr IAA

value: TBP


title: A2780_input


title: HCT116_H3K4Me1


title: ZRS/hs1516 Hindlimb ZPA, E11.5, replicate 3, ATAC-seq


title: HCT116_IAA_0hr_TBP_ChIP-seq

value: Doxycyclin


title: LUAD, normal, pair 39

description:
normal lung sample
205111140051_R05C01

value: normal

tag: age

value: female

value: II


title: LUAD, normal, pair 37

description:
normal lung sample
205049770040_R04C01

value: male

value: I


title: LUAD, normal, pair 38

description:
normal lung sample
205049770040_R07C01


title: 2571420_ATACseq_TCR_sgBatf1

tag: tissue

value: Spleen and lymph nodes

value: ex vivo cultured nTreg cells

value: sgBatf in RosaCas9/+ Foxp3gfp

value: anti-CD3/anti-CD28 restimulation


title: LUAD, normal, pair 36

description:
normal lung sample
205049770040_R03C01

value: LUAD


title: LUAD, normal, pair 35

description:
normal lung sample
205049770040_R01C01


title: HCT116_H3K27Ac

tag: genotype

value: WT


title: HCT116_TAF2_ChIP-seq

value: TAF2 (custom-made)


title: HCT116_H3K4Me3

value: Colorectal carcinoma


title: HCT116_input


title: ZRS/hs72 Hindlimb ZPA, E11.5, replicate 4, ATAC-seq

data_processing:
Fastq files were trimmed and clipped using trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using the following options -q 20 --stringency 2 --clip_R1 16 --clip_R2 16. Reads were then aligned to the original mm10 genome assembly as well as to a modified version of the genome containing the corresponding insertion using bedtools getfasta (Quinlan & Hall, 2010).
Assembly: mm10 + custom chr5 (hs72/ZRS)

value: FVB (strain)

value: Hindlimb


title: ZRS/hs72 Hindlimb ZPA, E11.5, replicate 3, ATAC-seq


title: ZRS/hs1516 Hindlimb ZPA, E11.5, replicate 1, ATAC-seq

description: bw file contains data for all replicates.


title: HCT116_H3K18Ac


title: HR+/HER2-BC_17

city: Seoul

first: Kyung Yeon

last: Han

address: 81, Irwon-ro, Gangnam-gu

country: South Korea

institute: Samsung Genome Institute, Samsung Medical Center

description: 10x Genomics

data_processing:
Gene counting and align using cellranger-4.0.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: primary breast cancer

extract_protocol:
Tumor tissues were mechanically dissociated and enzymatically digested on the day of surgery. Single-cell suspensions were collected after the removal of large pieces of debris using cell strainers. Dead cells were removed using Ficoll-Paque PLUS (GE Healthcare).
Libraries were prepared according to 10x Genomics Chrmoium Next GEM Single Cell 3' GEM Kit (ver.2) instructions.

value: primary breast cancer

tag: breast cancer_subtype

tag: patient

tag: Sex

value: Female

value: surgical excision without prior treatment


title: ZRS/hs72 Hindlimb ZPA, E11.5, replicate 2, ATAC-seq

tag: cell type


title: HR+/HER2-BC_14

description: 10x Genomics

tag: treatment


title: STRIPE-seq_Cold_3h_Rep4

data_processing:
The reads were aligned using STAR v2.7.10a with parameters --outSAMmultNmax 1, --alignEndsType Extend5pOfRead1.
The reads that aligned below mapping quality of 10 were filtered out using samtools v1.6.
The strand specific coverage was calculated using bedtools (v2.30) genomecov
Assembly: EnsemblePlants v6.54
Supplementary files format and content: Normalised read counts in bedgraph format

extract_protocol:
Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) and treated with Turbo DNase (ThermoFisher Scientific) according to manufacturers’ instructions. DNase-treated RNA was recovered by acid–phenol extraction and ethanol precipitation.
Libraries were constructed according to the protocol mentioned in Policastro et al. 2023.

value: Shoot

value: cold (4 C)

value: 3 hours

tag: protocol

value: STRIPE-seq


title: LUAD, normal, pair 32

description:
normal lung sample
205049770058_R06C01

tag: paired tissue

tag: sample type

value: normal

value: female

value: I


title: ZRS/LacZ Hindlimb ZPA, E11.5, replicate 3, ATAC-seq

data_processing:
Fastq files were trimmed and clipped using trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using the following options -q 20 --stringency 2 --clip_R1 16 --clip_R2 16. Reads were then aligned to the original mm10 genome assembly as well as to a modified version of the genome containing the corresponding insertion using bedtools getfasta (Quinlan & Hall, 2010).
Assembly: mm10 + custom chr5 (LacZ/ZRS)

value: ZRS^LacZ/WT


title: ZRS/hs72 Hindlimb ZPA, E11.5, replicate 1, ATAC-seq


title: LUAD, normal, pair 33

description:
normal lung sample
205111140038_R05C01

data_processing:
genomestudio software 1.0
Matrix process.txt = normalized (Beta MIxture Quantile dilation, BMIQ) Average Beta
Matrix signal intensities.txt = Unmethylated and methylated signal intensities

value: LUAD

tag: disease state

value: male

tag: t grade


title: HR+/HER2-BC_15

description: 10x Genomics


title: HCT116_IAA_24hr_TBP_ChIP-seq

tag: cell line

value: mAID knockin at TAF2 locus, rtTA3 expressing, Doxycline-inducible expression of OsTIR1

value: Doxycyclin and 24 hr IAA

value: TBP


title: LUAD, normal, pair 31

description:
normal lung sample
205049770058_R05C01

tag: Stage


title: HR+/HER2-BC_11

description: 10x Genomics


title: LUAD, normal, pair 30

description:
normal lung sample
205049770058_R04C01


title: STRIPE-seq_Cold_3h_Rep2

tag: cultivar

value: WT

tag: time


title: HR+/HER2-BC_08

description: 10x Genomics

value: primary breast cancer

tag: age


title: ZRS/LacZ Hindlimb ZPA, E11.5, replicate 2, ATAC-seq

tag: tissue

value: FVB (strain)

value: Hindlimb

tag: read size


title: ZRS/LacZ Hindlimb ZPA, E11.5, replicate 1, ATAC-seq

tag: genotype


title: HR+/HER2-BC_12

description: 10x Genomics

tag: breast cancer_subtype

tag: patient

value: Female

value: surgical excision without prior treatment


title: STRIPE-seq_Cold_3h_Rep1

value: Shoot

value: cold (4 C)

value: 3 hours


title: STRIPE-seq_WT_Rep4

value: STRIPE-seq


title: LUAD, normal, pair 34

description:
normal lung sample
205111140038_R08C01

value: normal

tag: Sex

value: female

value: IV


title: LUAD, normal, pair 29

description:
normal lung sample
205111140038_R01C01

value: LUAD

value: II


title: Hindlimb, E11.5, ATAC-seq

library_source: other

data_processing:
Fastq files were aligned to the mm10 genome assembly and barcodes counted using CellRanger ARC (v2.0.2) (Satpathy et al., 2019). Expression count and chromatin peak matrices generated from CellRanger were further processed using the Signac R package
Assembly: mm10

molecule: other

extract_protocol:
Single cell multiome ATAC-seq/RNA-seq was performed using a modified 10X protocol (10X Genomics, protocol CG000169 Rev D). Wild type mouse embryos were harvested at embryonic day E11.5. A single hindlimb bud was dissected in ice-cold PBS and incubated with collagenase II (Gibco, #17101015, 0.2 uL at 100 u/ul) for 10 min at 37 C. Every five minutes, hindlimb tissue was triturated using a P200 pipette for mechanical dissociation into single cells. Immediately after collagenase treatment, 10% FBS (450 uL) was added and dissociated cells were spun down. Supernatant was removed and cells were resuspended in 100 uL of ice-cold 10X nuclear lysis buffer (10X Genomics, protocol CG000169 Rev D) and incubated for 5 min on ice. Ice-cold wash buffer was then added and lysed cells were centrifuged and supernatant removed. Nuclei were resuspended in ice-cold wash buffer, quantified, and inspected for viability using Trypan Blue assay (Bio-Rad, 1450013).
10X Chromium Single Cell Multiome ATAC + Gene Expression kit (10X Genomics, 1000285)

tag: cell type


title: HR+/HER2-BC_05

description: 10x Genomics

tag: treatment


title: Hindlimb, E11.5, snRNA


title: HR+/HER2-BC_03

description: 10x Genomics


title: LUAD, normal, pair 28

description:
normal lung sample
205049770058_R03C01

tag: paired tissue


title: LUAD, normal, pair 27

description:
normal lung sample
205062750027_R07C01

tag: sample type

value: I


title: STRIPE-seq_Cold_3h_Rep3

tag: protocol


title: MPL-Calr(del52) Bone Marrow 5

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

data_processing:
Paired fastq files were processed with cellRanger (6.1.2) with the transcriptome index from Mouse mm10 (2020-A) downloaded from 10xgenomics website.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

growth_protocol: Donor mice are treated with 5-FU. Donor bone marrow are isolated on day four after treatment and cultured in RPMI, 10%FCS, 1%P/S supplemented with IL-3 (10ng/ml), IL-6 (10ng/ml) and mSCF (14ng/ml). EV or MPL+Calr(del52) expression constructs are transduced using a retroviral vector system with polybrene to increase transduction efficiency.

extract_protocol:
Bone marrow cells were isolated from femur, tibia and hip bone on day 21 past BMT. Erythrocytes were removed using erythrocyte lysis buffer. Cells were strained through a 75 µm cell strainer to receive single cell suspension. For all steps cells were treated according to 10xGenomics  Cell preparation guidelines.
Samples were processed using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Dual Index – 10x Genomics) following manufactures protocol. In short: GEM´s were generated using a Chromium Controller (10x Genomics) at a target cell recovery rate of 10.000. GEM-RT and subsequent clean-up was performed. cDNA was amplified and 3’ Gene Expression Dual Index Library Construction was performed. Illumina paired-end, dual indexing was performed. For all amplification steps a Veriti 96 Well Thermal Cycler (appledbiosystems) and for all quality control steps a 2200 TapeStation (Agilent Technologies) was used.

treatment_protocol: Mice received sub-lethal total body irradiation and subsequent bone marrow transplantation (100.000 transduced cells + 1*10^6 wt BM cells). On day 10 past transplantation blood was taken to check for engraftment and on day 21 past TP bone marrow was isolated

value: bone marrow

value: total BMC

value: mixed WT and MPL-Calr(del52)

value: TBI + BMT

tag: strain

value: Balb/cAnN


title: STRIPE-seq_WT_Rep2

value: WT


title: STRIPE-seq_WT_Rep1


title: LUAD, normal, pair 26

description:
normal lung sample
205049770058_R02C01

tag: disease state

value: male

tag: t grade


title: LUAD, normal, pair 25

description:
normal lung sample
205049770058_R01C01

tag: Stage


title: MPL-Calr(del52) Bone Marrow 3

tag: cell line


title: HSC, old, homeostasis, 4

city: Berkeley

first: Danica

state: California

address: 130 Hilgard Way,

department: NST

institute: UC Berkeley

data_processing:
Data analysis was processed within the Galaxy public server  (usegalaxy.org). In brief, after removing low-quality reads and adaptor sequences, data were mapped against mouse genome (mm10) using “HISAT2” (Galaxy Version 2.2.1) . Gene expression levels were measured from feature counts using “HTSeq” (Galaxy Version 0.9.1). Differential gene expression was analyzed using “DESeq2” (Galaxy Version 1.34.0).
Assembly: mm10
Supplementary files format and content: text file including raw counts for each sample

source_name: HSCs

extract_protocol:
Total RNA was extracted with RNeasy Plus Micro kit  (Qiagen) following the manufacture instruction.
RNA-sequencing libraries were prepared using QuantSeq  3’ mRNA-Seq Library Prep Kit FWD (Lexogen)

value: HSCs

value: KO

value: freshly isolate


title: LUAD, normal, pair 24

description:
normal lung sample
205103220094_R01C01

extract_protocol: genomic DNA was extracted and purified from LUAD samples using QIAamp DNA mini kit according to standard instructions

tag: age


title: HSC, old, homeostasis, 3


title: HR+/HER2-BC_06

description: 10x Genomics

value: primary breast cancer

value: Female

value: surgical excision without prior treatment


title: HSC, old, homeostasis, 2


title: Empty vector Bone Marrow 3

tag: tissue

value: EV-BM

value: mixed WT and EV


title: Cold_3h

data_processing:
Guppy was used for the basecalling of reads
Minimap2 was used to align the long reads to the reference genome with parameters "-ax splice -uf -k14 -L --cs --secondary=no"
bed files are generated with R
Assembly: EnsemblePlants v6.54
Supplementary files format and content: Genomic alignments with read counts in bed format

extract_protocol:
Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) and treated with Turbo DNase (ThermoFisher Scientific) according to manufacturers’ instructions. DNase-treated RNA was recovered by acid–phenol extraction and ethanol precipitation.
Total RNA was subjected to Poly-A enrichment and libraries were prepared for Direct RNA-Seq using SQK-RNA002 kit following manufacturer's protocol.

tag: cultivar

value: Shoot

value: cold (4 C)

tag: time

value: 3 hours


title: LUAD, normal, pair 23

description:
normal lung sample
205113580126_R08C01

value: LUAD

value: normal

value: I


title: HSC, old, homeostasis, 1

tag: genotype


title: LUAD, normal, pair 22

description:
normal lung sample
205062750039_R01C01

value: IV


title: Empty vector Bone Marrow 2

value: bone marrow

value: total BMC

value: TBI + BMT

value: Balb/cAnN


title: STRIPE-seq_WT_Rep3

value: WT

value: STRIPE-seq


title: WT


title: HSC, young, ex vivo, 4

value: HSCs

value: KO

value: cytokine stimulation


title: HSC, young, ex vivo, 3


title: HSC, young, ex vivo, 2


title: LUAD, normal, pair 21

description:
normal lung sample
205049770040_R06C01

value: male


title: LUAD, normal, pair 20

description:
normal lung sample
205062750001_R08C01

value: III


title: LUAD, normal, pair 19

description:
normal lung sample
205062750001_R07C01


title: HSC, young, ex vivo, 1


title: HSC, young, homeostasis, 4

value: freshly isolate


title: LUAD, normal, pair 18

description:
normal lung sample
205111140038_R06C01


title: 32D-MPL-Calr(ins5) 1

type: RNA

description: Gene expression from WT mouse CXCL12-abundant reticular cells

hyb_protocol: Labeled fragments were hybridized to Applied Biosystems Clariom S Mouse Arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization Oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: cell line generated from bone marrow of C3H mice

label_protocol: We used the Affymetrix WT Pico kit for cDNA synthesis, amplification, cRNA synthesis, second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin according to manufacturer's instructions.

growth_protocol: cells were cultured at 37°C, 5% CO2, in RPMI supplemented with 10% FCS, 1% P/S and 5ng/ml IL3

extract_protocol: Cell were washed with PBS to remove any IL3 and cultured over night. Cell were harvested from overnight culture and total RNA was isolated using QIAzol method.

treatment_protocol: 32D cells were transduced with MPL and Calr (WT or ins5). Cells were starved from IL3 over night in RPMI+FCS+P/S.

value: murine 32D

tag: lineage

value: myeloid

tag: transduced protein

value: MPL, Calr(ins5)


title: HSC, young, homeostasis, 2

tag: cell type


title: LUAD, normal, pair 17

description:
normal lung sample
205062750001_R06C01

value: LUAD

value: normal

tag: Sex

value: female

value: II


title: 32D-MPL-Calr(ins5) 5

value: bone marrow


title: 32D-MPL-Calr(ins5) 3


title: HSC, young, homeostasis, 3

tag: treatment


title: LUAD, normal, pair 16

description:
normal lung sample
205113580134_R07C01

tag: paired tissue

tag: sample type

value: I


title: HSC, young, homeostasis, 1

value: WT


title: LUAD, normal, pair 15

description:
normal lung sample
205113580134_R04C01


title: HCT116_shTAF2_R2

value: Colorectal carcinoma

value: 6 days


title: HCT116_shTAF2_R1


title: LUAD, normal, pair 13

description:
normal lung sample
205062750057_R02C01


title: HCT116_shScr_R1

value: shScramble


title: 32D-MPL-Calr(WT) 1

value: MPL, Calr(WT)


title: HCT116_shScr_R2


title: 32D-MPL-Calr(WT) 2


title: 32D-MPL-Calr(WT) 3


title: LUAD, normal, pair 12

description:
normal lung sample
205062750039_R06C01


title: 32D-MPL-Calr(ins5) 6


title: ATAC-YF_T-iTr-AA2P Replicate 2

data_processing:
100 bp paired-end reads obtained from all samples were trimming for Nextera adapter by cutadapt(version 1.9, paired-end mode, default parameter with “ -m 25 -O 6 ”) and aligned to mouse genome mm9 (MGSCv37 from Sanger) by BWA (version 0.7.12-r1039, default parameter), duplicated reads were then marked with biobambam2 (version v2.0.87) and only non-duplicated proper paired reads were chosen by samtools (parameter “-q 1 -F 1804” version 1.2).
Both Tr and iTr samples have more than 20 million fragments smaller than 2kb.
We adjust Tn5 shift (reads were offset by +4 bp for the sense strand and -5 bp for the antisense strand) and separated reads into nucleosome free, mononucleosome, dinucleosome, and trinucleosome by fragment size. We generated bigwig files by using the center of fragments and scale to 20 million nucleosome free reads. We observed good pattern that nucleosome tracks surrounded nucleosome free tracks, we provided nucleosome free tracks here since they are more informative.
Genome_build: mm9(MGSCv37 )
Supplementary_files_format_and_content: bigwig

source_name: Male mice

growth_protocol: Regulatory T (Tr) cells were FACS sorted from male Foxp3-gfp reporter mice by GFP expression and used for ATAC sequencing without in vitro culture. CD4 naïve T cells from male Foxp3-gfp reporter mice were used to induce regulatory T cells in vitro (iTr) by plate-bound anti-CD3 and anti-CD28 antibodies, recombinant Interleukin-2 (IL-2), and TGF-beta, and ascorbic acid-2-phosphate. Four days later, iTr cells were sorted by GFP expression for ATAC sequencing.

extract_protocol:
Sorted cells were harvested by centrifugation before being permeabilized for Tn5 transposition according to published protocols (PMID: 25559105).
Library was constructed according to published protocols (PMID: 25559105).

treatment_protocol: iTr cells were treated with 0.25 mM ascorbic acid 2-phosphate for 4 days during Treg induction to induce Tet-mediated DNA demethylation naturally occurring during Tr differentiation in vivo.

tag: strain

value: Male

value: In vitro induced wild-type regulatory T cells (ascorbic acid treated)


title: ATAC-YF_T-iTr-AA2P Replicate 1


title: LUAD, normal, pair 11

description:
normal lung sample
205062750039_R03C01

tag: disease state

value: male

value: III


title: Treat 3 - Cotreatment

city: Newcastle

first: Behnaz

last: Khavari

address: University Dr

country: Australia

institute: University of Newcastle

description:
AH3
Read_Counts-Cotreatment.txt
Differential_Expression_Results-Cotreatment.txt

data_processing:
Reads Quality Control; Fastqc (v0.11.8)
Reads Trimming; Cutadapt (v2.10)
Reads Alignment to the Reference Genome; Bowtie2 (v2.4.1)
Reads Quantification (Counting); htseq-count (v0.7.2)
Differential Expression Analysis; edgeR (v3.6.1)
Genome_build: hg19
Supplementary_files_format_and_content: "Read Counts" files include miRNAs read counts generated by htseq-count for all samples of each treatment.
Supplementary_files_format_and_content: "Differential Expression Results" files contain edgeR output, including log2FC and FDR for each miRNA in each treatment.

source_name: Bone marrow-derived cell line SK-N-SH

growth_protocol: The human neuroblastoma SH-SY5Y cells were grown at a density of 20,000 cells/cm2 in 6-well plates, containing Dulbecco’s Modified Eagle’s Medium (DMEM) cell culture medium, which was supplemented with 10% foetal bovine serum (FBS), 2mML-glutamine, and 20 mM HEPES, and maintained in a 5% CO2 atmosphere at 37 °C.

extract_protocol:
Having cells lysed with 1 ml Trizol reagent and centrifuged with 200 µL chloroform, total RNA was trapped in an aqueous phase, and precipitated by adding 80 μg glycogen and 500 μL isopropanol, and an overnight incubation at −20 °C. RNA was finally dissolved in nuclease-free water.
QIAseq miRNA Library Kit and Illumina NextSeq 500 platform were used for small RNA library preparation and sequencing, respectively, by the Ramaciotti Centre for Genomics (UNSW Sydney, Australia).

value: Neuroblastoma

value: Treated


title: 32D-MPL-Calr(WT) 6

value: murine 32D

value: myeloid


title: LUAD, normal, pair 10

description:
normal lung sample
205062750001_R04C01

source_name: fresh tissue

value: LUAD

value: normal

tag: t grade


title: SUM159 cells, NOS2KO Clone 6

city: HOUSTON

first: HONG

last: ZHAO

state: Texas

address: 6670 Bertner Ave

institute: HOUSTON METHODIST HOSPITAL

data_processing:
Image analysis and base calling were conducted by the Control software. Raw sequence data (.bcl files) generated from the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
The STAR aligner uses a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed.
Assembly: GRCh38
Supplementary files format and content: *.counts.txt: Tab-delimited text files include counts.

growth_protocol: SUM159 cells used in this study were obtained from ATCC, authenticated by short tandem repeat profiling, used within three passages since thawing, tested negative for Mycoplasma, and authenticated by short tandem repeat (STR) profiling, and cultured in DMEM media containing 10% FBS (GenDepot) and 1% antibiotic-antimycotic reagent (GenDepot).

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on three flowcell lanes. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.

treatment_protocol: For the CRISPR knockout of NOS2, SUM159 cells were transfected with the NOS2 Double Nickase Plasmid (Santa Cruz Biotechnology). After puromycin selection, resistant clones were selected by immunoblotting for iNOS expression and nitrite/nitrate colorimetric assay (Sigma).

value: triple-negative breast cancer cell line


title: ATAC-YF_Tr Replicate 2

value: Ex vivo isolated Treg cells


title: LUAD, normal, pair 9

description:
normal lung sample
205062750027_R05C01

tag: Stage

value: II


title: LUAD, normal, pair 14

description:
normal lung sample
205062750001_R05C01


title: ATAC-YF_Tr Replicate 1


title: LUAD, normal, pair 8

description:
normal lung sample
205062750001_R03C01

value: I


title: SUM159 cells, NOS2KO Clone 5

tag: cell line


title: Treat 2 - Cotreatment

description:
AH2
Read_Counts-Cotreatment.txt
Differential_Expression_Results-Cotreatment.txt


title: SUM159 cells, Parental

value: Parental Control


title: Control 2 - Cotreatment

description:
AH-con2
Read_Counts-Cotreatment.txt
Differential_Expression_Results-Cotreatment.txt

value: Untreated


title: Treat 1 - Cotreatment

description:
AH1
Read_Counts-Cotreatment.txt
Differential_Expression_Results-Cotreatment.txt


title: AH609_glutamate3

city: Toledo

first: Isaac

last: Schiefer

state: OH

address: 3000 Arlington Ave

institute: University of Toledo

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.
The reads were trimmed using Cutadapt v2.3
The reads were evaluated with FastQC(v0.11.8) to determine quality of the data.
Reads were mapped to the reference genome Rnor_6.0 (ENSEMBL), using STAR v2.7.8a
assigned count estimates to genes with RSEM v1.3.3
Assembly: Rnor_6.0
Supplementary files format and content: fastq

organism: Rattus norvegicus

source_name: cortical cells

extract_protocol:
RNeasy Mini Kit (Qiagen, 74104)
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (catalog number E7760L)

value: cortical cells

value: Glutamate


title: Control 3 - Cotreatment

description:
AH-con3
Read_Counts-Cotreatment.txt
Differential_Expression_Results-Cotreatment.txt


title: LUAD, normal, pair 6

description:
normal lung sample
205113580134_R08C01

tag: age


title: Control 1 - Cotreatment

description:
AH-con1
Read_Counts-Cotreatment.txt
Differential_Expression_Results-Cotreatment.txt


title: LUAD, normal, pair 5

description:
normal lung sample
205062750001_R01C01


title: Treat 3 - Pretreatment

description:
HA3
Read_Counts-Pretreatment.txt
Differential_Expression_Results-Pretreatment.txt


title: IS141_glutamate3


title: AH609_3


title: LUAD, normal, pair 4

description:
normal lung sample
205111140038_R04C01


title: IS141_3


title: Treat 1 - Pretreatment

description:
HA1
Read_Counts-Pretreatment.txt
Differential_Expression_Results-Pretreatment.txt


title: Treat 2 - Pretreatment

description:
HA2
Read_Counts-Pretreatment.txt
Differential_Expression_Results-Pretreatment.txt


title: DMSO_glutamate3


title: LUAD, normal, pair 1

description:
normal lung sample
205103220100_R03C01


title: SUM159 cells, NOS2KO Clone 1


title: Control 2 - Pretreatment

description:
HA-con2
Read_Counts-Pretreatment.txt
Differential_Expression_Results-Pretreatment.txt


title: DMSO_3

value: DMSO


title: IS141_glutamate2


title: LUAD, normal, pair 2

description:
normal lung sample
205103220100_R05C01

value: male


title: IS141_2


title: LUAD, normal, pair 7

description:
normal lung sample
205062750001_R02C01

value: female


title: Control 1 - Pretreatment

description:
HA-con1
Read_Counts-Pretreatment.txt
Differential_Expression_Results-Pretreatment.txt

value: Neuroblastoma


title: AH236_glutamate_2


title: KPP, replicate 2, scRNA-seq

city: Houston

first: Chaohao

address: 1881 East Rd

institute: MD Anderson Cancer Center

description: 10x Genomics

data_processing:
Single-cell RNA-seq gene expression libraries were mapped to mm10 mouse reference (10x Genomics pre-built reference, mm10-2020-A) using Cell Ranger (v6.1.1, 10x Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Single cell suspensions were prepared following 10x Genomics Cell Preparation Guide. Briefly, mice lung tissues were harvested and cut into smaller pieces, then used pipette to extensively pipette up and down to get tissue mixture in DMEM medium containing 2% FBS. This mixture was filtered with a 70 μm nylon mesh strainer, centrifuged at 300 g for 10 mins, then resuspended in DMEM medium containing 2% FBS to get single cell suspension. The single cell suspension was further sorted to enrich immune cell populations, and this suspension was processed for single-cell sequencing. Cell viability was at least 95% for all samples. 10000 cells were targeted for sequencing and loaded onto a Chromium Controller (10x Genomics) for gel beads-in-emulsion formation.
Library preparation was conducted using Chromium Next GEM Single Cell 3’ Gene Expression Kit (v3.1, 10x Genomics) according to the manufacturer’s instructions.

tag: tissue

value: Lung

value: KPP

value: Tumor

value: LSL-KrasG12D/Trp53fl/fl/ Rosa26LSL-Plk1

value: Ad-Cre


title: KPP, replicate 1, scRNA-seq

description: 10x Genomics


title: KPP, replicate 3, scRNA-seq

description: 10x Genomics


title: plank_none_rep3

city: Minneapolis

first: Julia

last: Willett

state: Minnesota

address: 689 23rd Avenue SE, 4-149 Micro Research Facility

institute: University of Minnesota

data_processing:
Reads were trimmed using Trimmomatic and were imported into Rockhopper for alignment and quantification of differentially expressed genes.
Assembly: NC_017316
Supplementary files format and content: tab-delimited file includes raw counts and relative abundance for each transcript in each replicate and condition

organism: Enterococcus faecalis

growth_protocol: Enterococcus faecalis OG1RF was grown in TYPS/CBM for 6 hr

extract_protocol:
Planktonic and biofilm cells were collected by centrifuging and scraping cells off Aclar disks, respectively.  Total RNA was harvested using a Qiagen Rneasy kit with minor modifications.  Cells were resuspended in 200 μL TE buffer (10 mM Tris pH 8.0, 1 mM EDTA) supplemented with 30 mg/mL lysozyme and 500 U/mL mutanolysin and incubated at 37 oC for 10 min, after which RNA was extracted using a Qiagen RNeasy kit following manufacturer’s instructions.  Lysozyme and mutanolysin were purchased from Sigma. Residual genomic DNA was removed using Turbo DNase (Ambion) following the manufacturer’s protocol for two DNase treatments (rigorous method).
TruSeq stranded libraries were constructed

treatment_protocol: Cells were grown with or without arginine

value: planktonic


title: plank_arg_rep3


title: biofilim_none_rep3

value: biofilm


title: biofilm_arg_rep3


title: KP, replicate 2, scRNA-seq

last: Li

description: 10x Genomics

value: KP


title: LUAD, normal, pair 3

description:
normal lung sample
205103220099_R08C01

value: LUAD

value: normal

value: I


title: DMSO_2

value: cortical cells


title: KP, replicate 1, scRNA-seq

description: 10x Genomics


title: DMSO_glutamate2

value: Glutamate


title: AH236_3


title: 1484803_Foxp3_Traditional

description: Traditional ChIP

data_processing:
ChIP-seq data analysis: Single reads of 50 bp were mapped mouse genome mm9 (MGSCv37 from Sanger) by BWA (version 0.7.12-r1039, default parameter), duplicated reads were then marked with biobambam2 (version v2.0.87), and non-duplicated reads were chosen by samtools (parameter “-q 1 -F 1024” version 1.2).
We followed ENCODE guideline for quality control of our data. All our samples passed QC criterion and have more than 30M non-duplicated reads.
After assessing the data quality, we extended reads to fragment size (detected by SPP v1.1) and generated bigwig tracks (normalized to 15 million uniquely mapped reads) for visualization. We then called peaks using MACS2(version 2.1.1.20160309, parameters “--nomodel --extsize fragment size”). We confirmed the PSI samples were highly reproducible that > 90% of peaks in one replicate could be called in another.
Genome_build: mm9(MGSCv37 )
Supplementary_files_format_and_content: bigwig

growth_protocol: CD4 naïve T cells from male Foxp3-gfp reporter mice were sorted to induce regulatory T cells in vitro (iTr) by plate-bound anti-CD3 and anti-CD28 antibodies, recombinant Interleukin-2 (IL-2), and TGF-beta, and ascorbic acid-2-phosphate. Four days later, iTr cells were used for Foxp3 PSI or traditional ChIP sequencing.

extract_protocol:
For Foxp3-PSI ChIP, cell fixation and intracellular staining was performed with Foxp3 staining kit (eBioscience). After Foxp3 PSI reaction, cells were fixed with 1% methanol-free formaldehyde at room temperature for 5 min and then sonicated for enrichment of biotinylated chromatins with streptavidin beads. Precipitated DNA was released by proteinase K digestion, phenol: chloroform extraction, and 2-propanol precipitation. Traditional Foxp3 ChIP was conducted according to standard protocols (PMID: 23021222).
Libraries were constructed according to standard protocols for ChIP

value: Male

value: In vitro induced wild-type regulatory T cells

tag: chip antibody

value: Rabbit anti-Foxp3 (Abcam, ab150743)


title: plank_arg_rep2


title: AH236_2


title: Scr1 scRNAseq

city: Amsterdam

first: Evgenia

last: Salta

state: north holland

address: Meibergdreef 47

country: Netherlands

institute: Netherlands Institute For Neuroscience

data_processing:
To confirm quality of the raw reads, a FastQC analysis (Version 0.11.5, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was performed. Reads were aligned to the mouse mm10 genome (Ensembl Version 88) using STAR (Version 2.5.2 (23104886)) with default options. A count table was generated from the alignments using Subread/FeatureCounts 1.5.1.
The count matrix was analyzed with Seurat 2.3.1, using the following workflow: Cells with less than 200 genes or more than 6,000 genes (likely doublets) were removed, as well as cells whose mitochondrial gene expression accounted for more than 20% of the total gene expression of that cell. Genes found in less than 0.5% of cells were also excluded. Following this filtering, 723 of the original 768 cells remained. Data were log-normalized and scaled by a factor of 10,000. The normalized count data subsequently regressed on the number of reads. Principal component analysis (PCA) was performed using the top 2000 highly variable genes. The first 15 PCAs were used to identify clusters (using default parameters). Data was visualized using Uniform Manifold Approximation and Projection (UMAP). Cluster markers were determined by a differential expression analysis of each cluster versus all other clusters combined (Supplementary Table 6). Literature markers (table S5 from Walgrave et al.) were used for cell type annotation. Gene differential expression between experimental (miR-132 knockdown) and control conditions (within each cell population) was performed (Supplementary Table 3). Differential expression (for analysis of cluster markers and for analysis between controls and experimental conditions) was performed as follows: p values were calculated using a Wilcoxon rank-sum test (using Seurat’s “FindMarkers” function) and corrected for multiple testing using a Bonferroni correction. Log fold changes were calculated using the natural logarithm. Genes with adjusted p values of < 0.05 were considered significantly differentially expressed.
Assembly: mm10
Supplementary files format and content: tab separated values and matrix files

source_name: dentate gyrus

extract_protocol:
FACS-sorted cells were processed using the Smart-seq2 protocol. Briefly, RNA was reverse-transcribed using biotinylated oligo-dT primers (IDT DNA, Belgium) and biotinylated template-switching (TSO) oligonucleotides (Exiqon, QIAGEN, Denmark) and subsequently cDNA was pre-amplified using the KAPA HiFi Hot Start DNA Polymerase (KAPA Biosystems, Roche Diagnostics, Belgium) and biotinylated ISPCR primers (IDT DNA, Belgium). cDNA was purified using AMPURE XP Agencourt beads (Beckman Coulter, France), concentration was calculated with the Quantifluor dsDNA kit (Promega, Netherlands) and adjusted on an Echo 525 Liquid Handler (Labcyte, CA, USA).
100 pg cDNA per cell were used for library preparation with Nextera XT DNA Library Preparation Kit (Illumina, CA, USA).
Following purification on magnetic beads the libraries were multiplexed and sequenced using the Illumina NextSeq500 platform (Illumina, CA, USA).

treatment_protocol: I.c.v. injections were performed using the following stereotactic coordinates: AP-0.1 mm, ML-1.0 mm, and DV-3.0 mm (from the skull). For miR-132 knockdown, 2-month-old nestin-GFP were infused with 2 ul of miR-132 antagomir, Ant-132 [locked nucleic acid (LNA)-, cholesterol-modified oligonucleotide] (Exiqon, QIAGEN, Denmark) at 0.33 nmol/ml in artificial cerebrospinal fluid (aCSF) (Harvard Apparatus, USA). Control mice received a scrambled LNA oligonucleotide in aCSF (Scr). Analysis of antagomiR-132-injected animals was performed at 3 months of age. Randomization of injectates was employed for all injection sessions, and animals were randomly allocated to each treatment.

value: dentate gyrus

value: male

value: nestin-GFP

value: Scr control-injected


title: Antagomir2 scRNAseq

value: miR-132 antagomir-injected


title: AH236_glutamate2


title: NK92_HS_HSF1_IP_2

city: New York

first: Kathryn

middle: Grace

last: Hockemeyer

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

data_processing:
Reads were aligned to the Homo Sapiens genome using the Bowtie2 aligner (Langmead et al., 2009) (v2.3.4.1).
Duplicate reads were removed using sambamba markdup.
Peaks were determined algorithmically using Model-based Analysis of ChIP-Seq 2 algorithm (v1.4.2) with q < 0.05.
Peak annotation was performed using ChipSeeker (Yu et al., 2015).
Assembly: hg38
Supplementary files format and content: Bed files of genomic regions of HSF1 peaks and summits
Supplementary files format and content: Annotated peak files of genomic regions of HSF1 peaks and summits

source_name: NK-92 MI cells

growth_protocol: NK-92 MI were maintained in αMEM without ribonucleosides and deoxyribonucleosides (Gibco) but containing 1.5 g/L sodium bicarbonate, 12.5% (v/v) horse serum (Gibco), 12.5% (v/v) FBS, 1% (v/v) GlutaMAX (Gibco), 0.2 mM inositol (Sigma), 0.1 mM β-mercaptoethanol (Gibco), and 0.02 mM folic acid (Sigma).

extract_protocol:
Cells were washed in 1XPBS and fixed with 1% formaldehyde for 10 min at room temperature. Subsequent steps until elution used 1x protease inhibitor. Nuclei were isolated on ice using nuclei isolation buffer for 5 minutes, with additional 5 min incubation with NP-40 0.3%. The cell pellet was lysed on ice using nuclei lysis buffer. Samples were sonicated using Covaris sonication. Clarified samples were transferred to Eppendorf tubes and diluted 1:10 with IP dilution buffer. Samples were precleared with 25 µl Protein A by rotation at 4°C for 1h. Supernatants were transferred to fresh tubes, and antibody was added and incubated overnight at 4°C. The next day, 25 µl of Protein A Dynabeads were added and samples were rotated at 4°C for 3 hours. After bead captures, beads were washed twice sequentially in each of. The following buffers: low salt wash buffer, high salt wash buffer, LiCl wash buffer, and TE. Samples were eluted and treated with RNase at 37°C for 30 minutes. Crosslinks were reversed overnight with the addition of proteinase K 0.5 mg/ml and 0.5% SDS. DNA was isolated using phenol/chloroform extraction followed by precipitation with ethanol and glycogen.
Libraries were prepared using the Swift biosciences DNA low-input library kit

treatment_protocol: 10 million cells were heat shocked at 42°C for 1 hour prior to use

value: NK-92 MI cells

value: wild-type

value: Heat shock followed


title: DMSO

value: DMSO


title: Scr2 scRNAseq


title: biofilm_arg_rep2

value: biofilm


title: AH609_glutmate2


title: CPT1 sg2, rep2

city: shanghai

first: Xiaolan

middle: Phenome

last: Zhou

state: State

address: Songhu road

institute: fudan

data_processing:
The raw paired-end reads obtained from RNA-seq experiments were filtering out low-quality reads, and then aligned to human reference genome sequence (UCSC hg38 assembly) using STAR with default settings. We used StringTie (-e -b) with the GENCODE reference transcriptome model to quantify the expression of all annotated genes. We choosed FPKM (fragments per kilobase of exon model per million reads mapped) to evaluate the gene expression level.
Assembly: hg38
Supplementary files format and content: NCIH460_CPT1_FPKM_matrix.xlsx.gz

source_name: Lung cell line

growth_protocol: NCI-H460 cells were maintained in RPMI 1640 medium (Invitrogen, catalog number 11875093) supplemented with 10% FBS and preserved at 37 °C in a humidified incubator containing 5% CO2.

extract_protocol:
Total RNA was extracted utilizing the TRIzol reagent (Invitrogen, catalog number 15596018), strictly adhering to the manufacturer's guidelines.
RNA libraries for RNA-seq were prepared using VAHTS mRNA Capture Beads（N401）+ VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina NR605-02,strictly adhering to the manufacturer's guidelines.

treatment_protocol: Lenti-CRISPRv2-KRAB-dSpCas9 (Addgene plasmid no. 139094)  was used to mediate gene interference.The plasmids was designed to express either nontargeting gRNA or gRNAs specifically targeting CPT1. Lentiviral particles were then produced in HEK293T cells, utilizing the psPAX2 and pMD2.G packaging vectors with Lipofectamine 2000. 48 hours after infection,NCI-H460 cells were selected and maintained in the presence of 2 μg/ml puromycin (Sigma, p8833).

value: Lung cell line

value: CPT1 knockdown


title: 3xCr; GPC6-4

first: Kwanha

last: Yu

address: One Baylor Plaza, BCM505

department: CAGT

institute: Baylor College of Medicine

data_processing:
Quality control was performed on fastq files using fastQC. Paired end reads were mapped to the mouse genome (mm10) using STAR (v2.5.0a).
Reads Per Million (RPM) were calculated using GenomicAlignments (v1.16.0) and DESeq2 (v1.20.0) was used for read count normalization and differential gene expression.
Assembly: mm10
Supplementary files format and content: csv file with normalized expression for each sample

source_name: brain

extract_protocol:
Bulk tissue was dissociated with QIAshredder column. RNA was isolated using trizol and chloroform and purified using the RNeasy Mini Kit (QIAGEN).
Illumina sequencing libraries were constructed from 500-900ng of total RNA using the TruSeq Stranded mRNA Library preperation kit (Illumina)

value: brain

value: neural


title: plank_none_rep2

value: planktonic


title: CPT1 sg2, rep1


title: AH236_glutamate

value: cortical cells

value: Glutamate


title: biofilim_none_rep2


title: AH609_2


title: 3xCr; GPC6-3


title: CPT1 sg1, rep1


title: CPT1 sg1, rep2


title: 3xCr; GPC6-1


title: 3xCr; GPC6-2


title: Liver_ST_Adar1flox/flox 2

city: Singapore

first: jinghe

last: xie

address: 21 Lower Kent Ridge Road

country: Singapore

institute: nuh

description: 10X Visium platform

data_processing:
space ranger
seurat
R in-house scripts
Library strategy: Spatial transcriptomics sequencing

source_name: Liver

extract_protocol:
Visium spatial gene expression kit (10x Genomics) was used. Briefly, immediately after mice were sacrificed, the livers were removed, cut into appropriately sized pieces, and embedded in OCT using an isopentane bath and liquid nitrogen. OCT sections were collected in a cryostat at 10µm per section. Three sections of each tissue were collected onto mRNA capture slides. Only samples with RIN quality more than 7 were used. Tissues were fixed in -20°C chilled methanol before H&E staining according to manufacturer’s protocol (CG000160 Rev B). Tissue optimization as performed according to manufacturer’s protocol to determine optimal permeabilization conditions (CG000238). Briefly, permeabilization enzyme was applied to H&E-stained tissues on optimization slide and a permeabilization time course was performed before fluorescent cDNA synthesis, tissue removal and slide imaging. All imaging was performed on EVOS M7000 imaging system (Thermo Fisher Scientific).
Tissue permeabilization was performed on Visium gene expression slides to release poly-adenylated mRNA from cells for capture by primers on ST spots underneath, followed by reverse transcription to generate barcoded full length cDNA. cDNA was amplified and cleanup performed using SPRIselect Reagent (Beckman Coulter, B23317). Library preparation was performed according to manufacturer’s protocol to generate libraries containing P5 and P7 Illumina primer sequences, Sample indexes i5 and i7 (10x, 3000431), TruSeq Read 1 and 2 sites, 10x Spatial Barcode, Unique Molecular Identifier (UMI), and inserts (CG000239 Rev D). 9 generated libraries were pooled and sequenced in one lane using Novaseq-6000 S4 for a depth of 2.5B total Paired end reads.

value: Liver

value: Ifih1-/- Adar1flox/flox Alb-Cre+

value: female

value: 8 weeks


title: AH236


title: CPT1 sgNTG, rep2

value: WT


title: DMSO_glutamate


title: Antagomir1 scRNAseq

value: dentate gyrus

value: male

value: nestin-GFP

value: miR-132 antagomir-injected


title: CPT1 sgNTG, rep1


title: AH609


title: Liver_ST_Adar1flox/flox 3

description: 10X Visium platform


title: AH609_glutamate


title: Liver_ST_Adar1wt/flox 3

description: 10X Visium platform

value: Ifih1-/- Adar1wt/flox Alb-Cre+


title: 3xCr-4

value: control


title: 3xCr-3


title: IS141


title: Liver_ST_Adar1wt/flox 2

description: 10X Visium platform


title: HCC_Tumor_scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Non-tumor and Tumor HCC liver tissues were gently dissociated by mechanical dissection to using forceps and scissors in Collagenase/Dispase (Roche 10269638001) over 2-3 hours at 37°C. Cells were then passed through a 100µm cell strainer and washed with 30ml Advanced DMEM/F12 (Gibco 12634-010) and centrifuged at 100g for 5 mins at 4°C. Red blood cells were lysed by resuspending cell pellet in RBC lysis buffer (Invitrogen 00-4333-57) for 1 minute, diluted with 30ml cold Advanced DMEM/F12 and centrifuged again. Cells were briefly washed cold Advanced DMEM/F12 containing 0.5U/ml RQ1 RNase-free DNaseI (Promega M6101), diluted with 30ml cold Advanced DMEM/F12 and centrifuged again. The live cells were resuspended in cold Advanced DMEM/F12, passed through a 40µm cell strainer to obtain single cell suspensions, and stained with trypan blue cell stain for viability assessment and manual cell counting prior to scRNA sequencing protocol.
10x Genomics Chromium Next GEM Single Cell 3’ kit v3.1 (Dual index) (CG000315 Rev A) was used according to manufacturer's protocol. Briefly, cell suspensions were loaded onto Chromium Next GEM Chip G for Gel-in-emulsion (GEM) generation at concentrations targeting 10,000 cells recovery per sample along with barcoded Single Cell 3’ V3.1 gel beads for poly-adenylated mRNA capture and partitioning oil. Only cell suspensions with more than 70% viability (determined by trypan blue stain) were used. Following GEM generation, partitioned cells were lysed and captured RNA were reverse transcribed to first-strand cDNA. GEMs were then broken and Dynabeads MyONE SILANE (10x, 2000048) were used for cleanup before full-length, barcoded cDNA was PCR amplified for library construction. Library preparation was performed according to manufacturer's protocol (CG000315 Rev A). This involved enzymatic fragmentation and size selection using SPRIselect Reagent (Beckman Coulter, B23317) to yield libraries containing P5 and P7 Illumina primer sequences, Sample indexes i5 and i7 (10x, 3000431), TruSeq Read 1 and 2 sites, 10x Barcode, Unique Molecular Identifier (UMI), and inserts. For human HCC scRNA sequencing experiments, 2 generated libraries were pooled and sequenced in one lane using HiSeq X for 367M total Paired end reads.

tag: disease

value: tumor HCC


title: Liver_ST_Adar1wt/flox 1

description: 10X Visium platform

tag: genotype


title: KO.-2 repl.-2

first: Manuel

last: Rogg

state: Baden Wuerttemberg

address: Breisacher Straße 115a

department: Institute of Surgical Pathology

institute: University Medical Center Freiburg

description: featureCounts: Counts; sgANXA4-2 repl.-2

data_processing:
The Galaxy Europe resource was used forprocessing and analysis of sequencing data (https://usegalaxy.eu).
Sequenced reads were quality and adapter trimmed using fastp v0.23.2.
Reads were mapped to hg38 whole genome using HISAT2 v2.2.1 with default settings for paired-end libraries.
featureCounts v2.0.1 and DESeq2 v2.11.40.8 were applied for differential expression analysis
Assembly: Human Dec. 2013 (GRCh38/hg38) (hg38)
Supplementary files format and content: tab-delimited text files include normalized counts for all samples

source_name: ANXA4 KO-2

growth_protocol: Cells were cultured in RPMI 1640 cell growth medium supplemented with Glutamine (Thermo Fisher Scientific, #61870036), 10 % FCS (Merck, #S0615) and Penicillin-Streptomycin (Thermo Fisher Scientific, #15140122), 95% air and 5% CO2. Equalized numbers of cell lines were seeded into cell culture dishes and cultured for 24 hours (non-confluent cell culture).

extract_protocol:
Cell were washed in PBS, scraped into PBS and pelleted by centrifugation. RNA was isolated from cell pellets using the Monarch Total RNA Miniprep Kit (T2010S, New England Biolabs) including gDNA depletion by gDNA binding columns and on column DNase-1 digest according to the supplier instructions. RNA quality number (RQN) was measured as >9.3 for all samples using an Agilent Fragment Analyzer system.
After polyA selection, RNA libraries were prepared for sequencing using the NEBnext ultra II RNA kit. Libraries were sequenced on the Illumina NovaSeq 6000 sequencer following the manufacturer's protocols.

tag: cell line_source

value: kidney cancer

value: ANXA4 knockout

value: ANXA4 KO-2

value: ANXA4 sgRNA-2


title: IS141_glutamate

value: cortical cells

value: Glutamate


title: KO.-2 repl.-1

description: featureCounts: Counts; sgANXA4-2 repl.-1


title: 3xCr-2

value: brain

value: neural


title: KO.-1 repl.-2

description: featureCounts: Counts; sgANXA4-1 repl.-2

source_name: ANXA4 KO-1

value: ANXA4 KO-1

value: ANXA4 sgRNA-1


title: KO.-1 repl.-1

description: featureCounts: Counts; sgANXA4-1 repl.-1


title: Liver_ST_Adar1wt/wt 3

description: 10X Visium platform

value: Liver

value: Ifih1-/- Adar1wt/wt Alb-Cre+

value: female

value: 8 weeks